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Biomedical Data Scientist Biostatistics | Nutrition | Microbiome

Biomedical data scientist with over 15 years of experience in nutrition, microbiome, and clinical research. My expertise combines biostatistics, multi-omics integration, and reproducible analytical workflows in R to translate complex biological data into actionable health insights.

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15+ Years Experience
35+ Publications
500+ Citations
30+ Clinical & Omics Datasets Analyzed
5K+ Samples analyzed
Biomedical Data Portfolio
Clinical Studies
R Data Analysis
Omics & Nutrition

Biomedical Data Scientist

Clinical & Nutrition Research • Microbiome • Statistical Analysis (R)

Sarah Chen
Amersfoort, Netherlands
Open to roles and collaborations

I am a biomedical data scientist with a background in Human Nutrition and microbiome research. My work focuses on integrating clinical, dietary, and multi-omics data to generate reproducible, evidence-based insights into human health.

Clinical research:

  • Experience with observational and interventional study designs, including real-world and clinical datasets
  • Focus on nutrition, microbiome, and metabolic health across diverse populations.

Data & analysis:

  • End-to-end analytical workflows from exploratory analysis to statistical modelling and interpretation.
  • Integration of multi-omics, clinical, and behavioral datasets to uncover biologically meaningful patterns
"

Where nutrition, biology, and microbiome research meet data science—translating complexity into insight through R.

Let's collaborate

I’m open to roles in clinical data science and biostatistics, as well as collaborations in microbiome and health-related research.

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Skills & Expertise

Statistical & Data Analysis

Clinical, epidemiological, and multi-omics data workflows

Study designs: observational (cross-sectional, case-control), randomized controlled trials, pragmatic trials

Statistical methods: linear & logistic regression, mixed-effects models, multivariate analysis

Analytical workflow: exploratory data analysis using multivariate approaches (PCA, PCoA, clustering) followed by targeted modelling and differential abundance analysis

Methodological rigor: confounding adjustment, multiple testing correction, power & sample size considerations

Data visualization:Time-series scatterplots with smooth trendlines, boxplots, alluvial plots, stacked bar charts, PCA/PCoA ordinations, and faceted visualizations using ggplot2 aesthetics (color, shape, fill, grouping)

Multi-omics & Biomedical Data

Microbiome, proteomics, and metabolic data integration

Microbiome data: 16S rRNA sequencing, shotgun metagenomics, diversity & compositional analysis

Proteomics: MaxQuant and Fragpipe-based workflows, protein annotation, differential expression, functional enrichment analysis

Clinical & metabolic data: clinical phenotypes, dietary intake, and continuous glucose monitoring (CGM)

Integrated datasets: Microbiome (16S rRNA, shotgun sequenced), proteomics, dietary intake, and continuous glucose monitoring (CGM); cross-study integration and multi-omics data harmonization

Programming & Reproducibility

Computational research workflows

R ecosystem

dplyr, ggplot2, phyloseq, vegan, microViz, maaslin, rstatix, plotly, flexdashboard, R Markdown

Workflow tools

Git/GitHub version control, reproducible pipelines, Linux (Bash)

Core Focus

Translating multi-omics and biomedical data into actionable insights for human health and metabolic research.

Analytical Tools
R (tidyverse, ggplot2)
Microbiome (phyloseq, vegan)
Multi-omics analysis
Bash / Linux (HPC)
Git / GitHub
R Markdown
Languages
Polish (native)
English (C1)
Dutch (B1)
Training & Courses
20+ DataCamp courses (R data analysis)
Statistical analysis in R (3 university courses)

Resume

Professional Experience

2022 - Present

Post-doc researcher

Wageningen University & Research (The Netherlands), Laboratory of Microbiology

Wageningen University & Research (The Netherlands), UNLOCK Facility (since 2023)

  • Designed and executed bioinformatics and statistical analyses of high-dimensional clinical and multi-omics datasets (16S, shotgun metagenomics, proteomics) using R, Bash, and HPC (Snellius).
  • Led statistical modeling and multivariate analyses for observational and interventional clinical studies on gut microbiota across infant, pediatric, and adult populations.
  • Contributed to development of statistical analysis plans (SAPs) for microbiome and clinical studies.
  • Built reproducible R-based data pipelines with Git/GitHub and R Markdown to ensure analytical traceability and validation readiness.
  • Collaborated cross-functionally with clinicians, microbiologists, and nutrition scientists to translate analytical outputs into biologically and clinically meaningful insights.
  • Supported internal training and development of reproducible data science workflows for microbiome research teams.
Statistical modelling in R Omics datasets integration Bash scripting Supervisors: Clara Belzer, Hauke Smidt
2020 - 2022

Post-doc researcher

Wageningen University & Research (The Netherlands), Human Nutrition Division

  • Applied regression modeling and confounding adjustment to evaluate diet–microbiome–health relationships in real-world observational datasets.
  • Integrated microbiome composition data with dietary intake and continuous glucose monitoring to investigate metabolic health associations.
  • Strengthened expertise in microbiome data analysis workflows, including processing and statistical interpretation of high-dimensional sequencing data.
  • Contributed to in vitro cell-based experimental research, supporting mechanistic interpretation of microbiome-related findings.
Microbiome analyses in R First author contributions Collaborators: Wilma T. Steegenga, Guido JEJ Hooiveld
2013 - 2022

Assistant professor

Poznań University of Life Sciences (Poland), Department of Human Nutrition and Dietetics

  • Led and co-investigated multiple funded projects on nutrition, gut microbiota, and metabolic health, generating real-world evidence from observational and experimental studies.
  • Designed statistical analysis strategies and performed multivariate and regression analyses for clinical and epidemiological datasets.
  • Worked with experimental datasets generated from wet lab workflows, including DNA extraction, PCR, ELISA, and HPLC-based assays, supporting downstream statistical and bioinformatics analysis.
  • Contributed to study design discussions
  • Supervised 40+ MSc/BSc theses in nutritional science, biostatistics, and microbiome data analysis.
  • Delivered lectures (English and Polish) on human nutrition, genomics, and quantitative data analysis.
Grant application Teaching Familiarity with wet lab techniques Supervisor: Agata Chmurzynska
MAY 2013 - JUNE 2013

Senior medical documentation specialist

Biofarm LLC (Poznań, Poland)

  • Synthesized clinical and scientific evidence to support regulatory documentation and substantiation of nutritional supplement products.
  • Collaborated cross-functionally with marketing teams to align scientific evidence with product communication and positioning.
  • Gained exposure to commercial and regulatory aspects of product development in the nutrition sector.
Business awareness
APRIL 2012 - JUNE 2012

Intern

Danone Research – Centre for Specialized Nutrition (Wageningen, The Netherlands)

  • Conducted laboratory and literature-based analyses on early-life nutrition and long-term metabolic health.
  • Contributied to interdisciplinary research discussions within specialized nutrition R&D teams.
Early-life nutrition research Science-to-product translation Supervisor: Annemarie Oosting

Education

Doctor of Philosophy (PhD)

Poznań University of Life Sciences / Faculty of Food Science and Nutrition

2008 - 2013

Thesis title: Genetic and nutritional determinants of folate metabolism in the elderly in terms of risk of cardiovascular diseases.

Master of Science (MSc)

Poznań University of Life Sciences / Faculty of Food Science and Nutrition

2003 - 2008

Thesis title: The influence of protein deficiency during the prenatal period on methylation of the Ppara gene in the rat.

Scientific Grants

The intestinal microbiota composition and development of preterm infants in early life

Investigator • 2022 - Present

  • Analyzed microbiome datasets (composition and diversity) derived from 16S rRNA sequencing and shotgun metagenomics.
  • Integrated datasets across projects and perform association analyses with clinical and experimental metadata.
  • Analyzed metaproteomic datasets using MaxQuant and Fragpipe, including database generation, protein annotation, and downstream expression and enrichment analyses.

The effect of galacto-oligosaccharides (GOS) or chicory fructo-oligosaccharides (FOS) versus a placebo on bowel habits in children with functional constipation (INSIDE study).

Research Data Analyst • 2025 - PRESENT

  • Cleaned and curated longitudinal clinical and microbiome datasets from a randomized, placebo-controlled, double-blind trial
  • Co-developed the Statistical Analysis Plan (SAP) in collaboration with study team members.
  • Performed statistical analysis of clinical and microbiome time-series data.
  • Contributed to manuscript writing and interpretation of study results.

The effect of a 6 weeks intervention with synbiotics on the recovery speed of the gut microbiota after antibiotic treatment in Dutch toddlers (TOBBI study).

Co-supervisor (PhD candidate) • 2023 - Present

  • Provide scientific and methodological input on study design, analytical strategy, and interpretation of findings.
  • Support manuscript development and critical scientific review.

FucoQuest: The impact of fucosylated human milk oligosaccharides on infant gut microbiome, metabolism and gut function.

Research Data Analyst • 2022 - PRESENT

  • Performed multi-omics analysis of infant gut microbiome.
  • Analyzed 16S rRNA and shotgun metagenomic data to characterize microbial composition.
  • Conducted functional profiling using HUMAnN to infer microbial metabolic pathways.
  • Analyzed metaproteomic datasets to assess functional protein-level activity and contributed to integrative interpretation across omics layers.

The effect of a multispecies probiotic on reducing the incidence of antibiotic-associated diarrhoea in children.

Investigator • 2023 - 2024

  • Analyzed microbiome sequencing data (16S rRNA) to asses the impact of a multispecies probiotic on antibiotic-associated diarrhoea in children.
  • Developed publication-quality visualizations of microbiome and clinical outcome data.
  • Contributed to interpretation of results, conclusions, and manuscript preparation.

Elucidating the role of human small intestine microbiota in explaining differences in postprandial glucose responses (GLYSIMI).

Investigator • 2021 - 2022

  • Analyzed continuous glucose monitoring (CGM) data from wearable sensors.
  • Integrated CGM with dietary intake records to assess postprandial glucose responses, including calculation of iAUC and related glycaemic metrics.

Influence of maternal choline intake and non-alcoholic fatty liver disease during pregnancy and lactation on endocrine pancreas development in the offspring.

Investigator • 2017 - 2022

  • Performed ELISA-based quantification of metabolic biomarkers (choline, insulin).
  • Contributed to scientific review of manuscripts and conference abstracts

Gut microbiota as the link between dietary patterns and human metabolism.

Principal investigator • 2016 - 2020

  • Led full project lifecycle from funding acquisition through study design, participant recruitment, dietary and laboratory analyses, statistical modeling, and dissemination of results via manuscripts.

Relationships between fat discrimination, frequency of eating high-fat foods, and gene polymorphism - determination of body weight and lipid metabolism.

Investigator • 2015 - 2019

  • Collected and analyzed dietary intake data to investigate associations between fat consumption patterns, eating behavior, and gene polymorphisms related to lipid metabolism.

Assessment of choline intake and choline metabolism in pregnant women.

Investigator • 2015 - 2019

  • Assessed choline and carnitine intake in pregnant women using dietary records, applying custom food composition tables not yet implemented in standard dietary assessment tools.

Relationship between choline gut metabolism and cardiovascular diseases.

Investigator • 2014

  • Estimated dietary choline intake and collaborated on integration with circulating biomarkers (TMA, TMAO, choline) to investigate links between gut metabolism and cardiovascular risk.

Genetic determinants of homocysteine metabolism.

Investigator • 2013

  • Analyzed CBS and MTHFR gene polymorphisms in laboratory settings.
  • Developed plasma homocysteine quantification
  • Integrated genetic, plasma homocysteine, and nutritional data (folate, B vitamins, dietary patterns) to investigate determinants of homocysteine metabolism.

Nutritional programming of metabolism in the rat: effects of maternal diet composition on offspring metabolic outcomes.

MSc Thesis Researcher • 2013

  • Contributed to an in vivo animal study (rat model).
  • Performed experimental work, including DNA extraction and assessment of PPARα gene methylation to investigate epigenetic effects of prenatal protein deficiency.

Portfolio

A selection of projects showcasing analysis of clinical, nutritional, and multi-omics datasets, including microbiome (16S rRNA sequencing), proteomics, and continuous glucose monitoring. These projects demonstrate data integration, statistical modelling, and reproducible workflows in R, with a focus on translating complex datasets into actionable insights. An interactive dashboard version of my CV is also available.

Each project is presented as a knitted HTML report from R Markdown, with links to full code available on GitHub.

  • All Work
  • Omics
  • Nutritional & Clinical
  • Other
Microbiome analysis and visualisation
Click to explore
Omics 2025

Amplicon sequencing tutorial using wetlands dataset

A complete amplicon sequencing workflow covering preprocessing, taxonomy assignment, diversity analysis, differential abundance testing, and publication-ready visualizations.

Glucose sensor scanning
Click to explore
Nutritional & Clinical 2022

Postprandial glucose response analysis using CGM and dietary data

Integration of continuous glucose monitoring (CGM) and dietary intake data to quantify postprandial responses and assess inter-individual variability. Conducted within the GLYSIMI project in collaboration with Human Nutrition & Health (WUR).

Protein molecule
Click to explore
Omics 2022

Proteomics analysis

Metaproteomic analysis of infant gut microbiomes to compare functional protein profiles between groups with distinct microbial compositions, including database construction, mass spectrometry processing, and statistical analysis.

Combining datasets Under Construction
Click to explore
Omics 2024

Gut microbiome analysis in preterm infants using integrated 16S rRNA datasets

Integration of 16S rRNA sequencing data from multiple cohorts of preterm infants to investigate gut microbiome composition and early-life developmental trajectories. The study focused on microbial succession and compositional changes within the first 60 days of life.

Creating CV
Click to explore
Other 2026

Resume on dashboard

Interactive CV dashboard combining timelines and visual summaries, including word clouds, to present research experience, analytical skills, and technical competencies in a structured and accessible format.

Dietary patterns Under Construction
Click to explore
Nutritional & Clinical 2020

Dietary patterns and adult health

Analysis of dietary patterns and their association with cardiovascular risk factors in adult populations using statistical modelling approaches to assess relationships between diet quality and health outcomes.

Contact

Let's Connect

I am open to collaborations in clinical data science, microbiome research, and multi-omics analytics.

Email me malino.anna@gmail.com
Location Amersfoort
Netherlands

Send me a message

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